You're right, I wouldn't want to get rid of any of the current espionage. It would just be nice if the presence of a defending probe team was a certain deterrent (until defeated) rather than the current, maybe-it-will-discover-an-enemy-probe-team-maybe-not system.
Well, if the presence of the probe team would increase capture chance... it does influence it, right? As combat, it's random, so you'll never have a guarantee. Anyway, since it's some time since this came up, I could think about it a bit and can explain better where's my gut-feeling coming from.
The problem with probe team vs. probe team combat is, from my point of view, rather complex:
1) It defeats the point of spies being invisible - this is either frustrating (you can see the teams, but your military units can't touch them) or makes them useless (if military units can get to them).
2) It's micromanagement for not a lot of gain - passive espionage defends you as well, but it's easier on the human player. Shuffling dozens of counter-spies around is annoying - and while you could say "it's like military", well, right. But it's not like it's replacing military, it's on top of that!
3) It forces you into the espionage game. Simply put, with spy combat, having spies becomes a defensive requirement - it forces you to build and position them, because ignoring that would only mean trouble. In the current espionage system, you can decide not to get involved into active espionage. Perhaps build some spies (in SuperSpies) as garrison, perhaps turn the espionage slider a notch up... that's it. This allows you to have a reasonable defence against the more disrupting actions - similar to the way a builder just keeps a small garrison to avoid getting munched up by warmongers.
4) It's a feel thing. Spies are single persons or small teams - it's nowhere near the unit scale. Units are dozen or hundreds of people, that's an entirely different scale. Having combat between spies feels like rehash of normal/psi combat. Without the combat, you get more of the feeling that it's a single spy, outside of the military scale, that is sneaking around, doing espionage.
Now, this doesn't mean that I think the BTS espionage system is perfect - I believe it can be greatly expanded, but along the tenets of its current design.
Cheers, LT.